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. 2020 Nov 16;9:e59157. doi: 10.7554/eLife.59157

Figure 2. CRMs controlling Ciinte.Ascl.b expression in VDML.

(A) Snapshot of the Ciinte.Ascl.b locus depicting ATAC-seq profile at mid-neurula stages, tested genomic regions, transcript models and conservation between C. robusta and C. savignyi (from https://www.aniseed.cnrs.fr/ and Dardaillon et al., 2020; Madgwick et al., 2019). (B–C) Representative examples of X-gal stained embryos at early tailbud stages following C. intestinalis embryos electroporation of Ciinte.Ascl.b-do1 (B) And Ciinte.Ascl.b-do5 (C). Embryos are shown in lateral view with dorsal to the top and anterior to the left. Scale bar: 100 μm. (D) Schematic representation of the various constructs and their activity at early tailbud stages in DML (blue) and VML (purple) (n indicates the total number of embryos examined; N indicates the number of independent experiments).

Figure 2.

Figure 2—figure supplement 1. Putative TFBS.

Figure 2—figure supplement 1.

Identification of putative TFBS for candidate upstream factors in Ciinte.Ascl.b-do2 aligned with its counterpart from C. savignyi. All putative sites for ventral factors (SBE, BRE, Tbx2/3, Nkxtun1, Nkx2-3/5/6 and Irx.c) and dorsal factors (Msx and Su(H)/Rbpj) have been mapped, but only conserved sites are shown: 2 SBE, 3 Tbx2/3, 2 Nkx2-3/5/6 and 2 Msx sites. The region important for VML expression (deleted in do4) contains 2 Tbx2/3 and 1 Nkx2-3/5/6 sites. Since Ascl.b is expressed after Msx (Roure and Darras, 2016), it could be directly regulated by Msx in both VML and DML. However, the region required for VDML activity (deleted in do3) contains a Tbx2/3 site. This suggest that Ascl.b expression relies on additional unidentified factors. Note that the size of the highlighted site for of a given TF may vary depending on the matrix used.